Chromosome sizes don't match

[sjb343]

Hi,

I'm having a heck of a time finding the chromosome sizes for mm9 that match the mm9 Bowtie pre-built indexes on their website. I have ChIP-seq data aligned using Bowtie2 to mm9 and used Macs2 to call peaks generating bedgraph files. Now I'm trying to convert these to BigWig files using bedgraphtobigwig but the UCSC chromosome sizes are not matching up. I can't find any threads with this problem but I'm not sure what I'm doing wrong. Since I can't seem to find anything, my questions is, is there a way to extract the chromosome sizes from the available Bowtie mm9 pre-built indexes?

Thanks,
sj

[dariober]

You can get chromosome sizes from UCSC with something like this (credit: bedtools docs):

mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e \
	"select chrom, size from mm9.chromInfo"  > mm9.genome

Then you could check if these sizes match the sizes used by bowtie2 to build the index (they should). I think the utility bowtie2-inspect with -s option should give you the chromosome lengths.

Finally, you could extract chrom sizes from the header of a bam file with e.g:

samtools view -H aln.bam \
    | grep -P "@SQ\tSN:" \
    | sed 's/@SQ\tSN://' \
    | sed 's/\tLN:/\t/' > genome.txt